It's generally recommended to adjust your system for performance when crunching. This is almost a necessity for GPU crunching, so disabling Aero, useless start-up processes and unnecessary background services helps. In particular it's a good idea to Adjust the System Performance:

Start, Right Click on computer, Properties, Advanced System Settings, under the Advanced Tab and the Performance section, select Settings and Adjust for Best Performance.

If that, and a few other things (in the FAQ's) doesn't resolve the issue, consider adjusting the registry settings for Timeout Detection,

http://msdn.microsoft.com/en-us/windows/hardware/gg487368

Note that this might lead to system crashes, so it's not recommended on production systems, and make sure your files are backed up if you use the system for anything else.
If you are experiencing this problem on 24/7 crunching rigs the Timeout Registry edit looks like a good fix. I've seen this and similar errors many times over last few years, and various workarounds (which don't always work; probably driver dependent). This looks like the best fix.

BTW. I think this can't be implemented into an app as it would infringe upon the MS Logo licence - otherwise it might have been done by a few projects.
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